Automated protein sequencing is an important tool in protein characterization. Most instruments use tetrahydrofuran (THF) as the HPLC eluent for separation of the derivatized amino acids residues. THF is highly perishable when exposed to air, generating peroxides which can degrade amino acids, mainly lysine, leading to uncertainty in chromatogram interpretations. Modifications of the existing HPLC equipment were introduced to create a permanent inert atmosphere inside the bottle of THF solution. This was carried out by changing the argon plumbing and some electrical connections and by reprogramming the software of the protein sequencer. The positive results of this procedure were demonstrated by comparing the decreasing lysine peak area during 28 days before and after the modifications. In the modified instrument, lysine recovery was much better as a function of the age of the THF eluent. Since these modifications improved the instrument performance, they have been adopted for routine use in our laboratory.